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Theobroma cacao and Theobroma grandiflorum: Botany, Composition and Pharmacological Activities of Pods and Seeds. Foods 2022; 11:foods11243966. [PMID: 36553708 PMCID: PMC9778104 DOI: 10.3390/foods11243966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Cocoa and cupuassu are evergreen Amazonian trees belonging to the genus Theobroma, with morphologically distinct fruits, including pods and beans. These beans are generally used for agri-food and cosmetics and have high fat and carbohydrates contents. The beans also contain interesting bioactive compounds, among which are polyphenols and methylxanthines thought to be responsible for various health benefits such as protective abilities against cardiovascular and neurodegenerative disorders and other metabolic disorders such as obesity and diabetes. Although these pods represent 50-80% of the whole fruit and provide a rich source of proteins, they are regularly eliminated during the cocoa and cupuassu transformation process. The purpose of this work is to provide an overview of recent research on cocoa and cupuassu pods and beans, with emphasis on their chemical composition, bioavailability, and pharmacological properties. According to the literature, pods and beans from cocoa and cupuassu are promising ecological and healthy resources.
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Cinar ZÖ, Atanassova M, Tumer TB, Caruso G, Antika G, Sharma S, Sharifi-Rad J, Pezzani R. Cocoa and cocoa bean shells role in human health: An updated review. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.104115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Jean-Marie E, Bereau D, Robinson JC. Benefits of Polyphenols and Methylxanthines from Cocoa Beans on Dietary Metabolic Disorders. Foods 2021; 10:2049. [PMID: 34574159 PMCID: PMC8470844 DOI: 10.3390/foods10092049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 02/08/2023] Open
Abstract
Theobroma cacao L. is an ancestral cultivated plant which has been consumed by various populations throughout history. Cocoa beans are the basic material occurring in the most consumed product in the world, namely chocolate. Their composition includes polyphenols, methylxanthines, lipids and other compounds that may vary qualitatively and quantitatively according to criteria such as variety or culture area. Polyphenols and methylxanthines are known as being responsible for many health benefits, particularly by preventing cardiovascular and neurodegenerative diseases. Recent studies emphasized their positive role in dietary metabolic disorders, such as diabetes and weight gain. After a brief presentation of cocoa bean, this review provides an overview of recent research activities highlighting promising strategies which modulated and prevented gastro-intestinal metabolism dysfunctions.
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Affiliation(s)
| | | | - Jean-Charles Robinson
- Laboratoire COVAPAM, UMR Qualisud, Université de Guyane, 97300 Cayenne, France; (E.J.-M.); (D.B.)
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Structural and Functional Genomics of the Resistance of Cacao to Phytophthora palmivora. Pathogens 2021; 10:pathogens10080961. [PMID: 34451425 PMCID: PMC8398157 DOI: 10.3390/pathogens10080961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 11/17/2022] Open
Abstract
Black pod disease, caused by Phytophthora spp., is one of the main diseases that attack cocoa plantations. This study validated, by association mapping, 29 SSR molecular markers flanking to QTL (Quantitative Trait Loci) associated with Phytophthora palmivora Butler (Butler) (PP) resistance, in three local ancient varieties of the Bahia (Comum, Pará, and Maranhão), varieties that have a high potential in the production of gourmet chocolate. Four SSR loci associated with resistance to PP were detected, two on chromosome 8, explaining 7.43% and 3.72% of the Phenotypic Variation (%PV), one on chromosome 2 explaining 2.71%PV and one on chromosome 3 explaining 1.93%PV. A functional domains-based annotation was carried out, in two Theobroma cacao (CRIOLLO and MATINA) reference genomes, of 20 QTL regions associated with cocoa resistance to the pathogen. It was identified 164 (genome CRIOLLO) and 160 (genome MATINA) candidate genes, hypothetically involved in the recognition and activation of responses in the interaction with the pathogen. Genomic regions rich in genes with Coiled-coils (CC), nucleotide binding sites (NBS) and Leucine-rich repeat (LRR) domains were identified on chromosomes 1, 3, 6, 8, and 10, likewise, regions rich in Receptor-like Kinase domain (RLK) and Ginkbilobin2 (GNK2) domains were identified in chromosomes 4 and 6.
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Mariatti F, Gunjević V, Boffa L, Cravotto G. Process intensification technologies for the recovery of valuable compounds from cocoa by-products. INNOV FOOD SCI EMERG 2021. [DOI: 10.1016/j.ifset.2021.102601] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Apraez Muñoz JJ, de Almeida AAF, Pirovani CP, Ahnert D, Baligar VC. Mitigation of Pb toxicity by Mn in seedling of the cacao clonal CCN 51 genotype grown in soil: physiological, biochemical, nutritional and molecular responses. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:240-256. [PMID: 33528689 DOI: 10.1007/s10646-021-02348-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
Lead (Pb) is a highly toxic metal for humans, animals and plants even at low concentrations in the soil. The ingestion of chocolate produced from contaminated beans can contribute to consumer exposure to Pb. While, Mn is an element essential for plants and participates as enzymatic cofactors in several metabolic pathways. The objective of this study was to evaluate the influence of Mn on mitigation of Pb toxicity in seedling of the cacao clonal CCN 51 genotype grown in soils with different doses of Pb, Mn and Mn+Pb, through physiological, biochemical, molecular and nutritional responses. It was found that the seedling of the cacao clonal CCN 51 genotype grown in soils with high Pb, Mn and Mn+Pb contents accumulated these heavy metals in the roots and leaves. Mn doses reduced the Pb uptake by root system and prevented that the Pb accumulated at toxic levels in the roots and leaves of the plants. High doses of Pb applied in soil were highly toxic to the plants, leading, in some cases, them to death. However, no Mn toxicity was observed in cocoa plants, even at high doses in the soil. Uptake of Pb and Mn by the roots and its transport into the aerial part of the plant promoted changes in photosynthesis, leaf gas exchange, respiration, carboxylation and in the instantaneous efficiency of carboxylation, reducing in the treatments with the highest concentrations of Pb, and the emission of chlorophyll fluorescence, affecting the efficiency of photosystem 2 and the production of photoassimilates. Besides that, Pb, Mn and Mn+Pb toxicities activated defense mechanisms in plants that alter the gene expression of met, psbA and psbO, increasing in plants subjected to high concentrations of Pb and the activity of the enzymes involved in the cellular detoxification of excess ROS at the leaf level. In addition, high uptake of Mn by root system was found to reduced Pb uptake in plants grown with Mn+Pb in the soil. Therefore, application of Mn in the soil can be used to mitigate the Pb toxicity in seedling of the cacao clonal CCN 51 genotype grown in contaminated soils.
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Affiliation(s)
- Jose Julian Apraez Muñoz
- State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900, Ilhéus, BA, Brazil.
| | - Alex-Alan Furtado de Almeida
- State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900, Ilhéus, BA, Brazil
| | - Carlos Priminho Pirovani
- State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900, Ilhéus, BA, Brazil
| | - Dário Ahnert
- State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900, Ilhéus, BA, Brazil
| | - Virupax C Baligar
- USDA-ARS-Beltsville Agricultural Research Center, Beltsville, MD, USA
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Díaz-Valderrama JR, Leiva-Espinoza ST, Aime MC. The History of Cacao and Its Diseases in the Americas. PHYTOPATHOLOGY 2020; 110:1604-1619. [PMID: 32820671 DOI: 10.1094/phyto-05-20-0178-rvw] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cacao is a commodity crop from the tropics cultivated by about 6 million smallholder farmers. The tree, Theobroma cacao, originated in the Upper Amazon where it was domesticated ca. 5450 to 5300 B.P. From this center of origin, cacao was dispersed and cultivated in Mesoamerica as early as 3800 to 3000 B.P. After the European conquest of the Americas (the 1500s), cacao cultivation intensified in several loci, primarily Mesoamerica, Trinidad, Venezuela, and Ecuador. It was during the colonial period that cacao diseases began emerging as threats to production. One early example is the collapse of the cacao industry in Trinidad in the 1720s, attributed to an unknown disease referred to as the "blast". Trinidad would resurface as a production center due to the discovery of the Trinitario genetic group, which is still widely used in breeding programs around the world. However, a resurgence of diseases like frosty pod rot during the republican period (the late 1800s and early 1900s) had profound impacts on other centers of Latin American production, especially in Venezuela and Ecuador, shifting the focus of cacao production southward, to Bahia, Brazil. Production in Bahia was, in turn, dramatically curtailed by the introduction of witches' broom disease in the late 1980s. Today, most of the world's cacao production occurs in West Africa and parts of Asia, where the primary Latin American diseases have not yet spread. In this review, we discuss the history of cacao cultivation in the Americas and how that history has been shaped by the emergence of diseases.
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Affiliation(s)
- Jorge R Díaz-Valderrama
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, U.S.A
| | - Santos T Leiva-Espinoza
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Amazonas, Perú
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, U.S.A
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Gopaulchan D, Motilal LA, Kalloo RK, Mahabir A, Moses M, Joseph F, Umaharan P. Genetic diversity and ancestry of cacao ( Theobroma cacao L.) in Dominica revealed by single nucleotide polymorphism markers. Genome 2020; 63:583-595. [PMID: 32853534 DOI: 10.1139/gen-2019-0214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cacao (Theobroma cacao L.), an introduced tree crop in Dominica, is important for foreign exchange earnings from fine or flavour cocoa. The genetic structure of farmed cacao in Dominica was examined to identify varieties for conservation, breeding, and propagation to improve their cocoa industry. Cacao trees (156) from 73 sites over seven geographical regions were genotyped at 192 single nucleotide polymorphism (SNP) markers. Identity, regional differentiation, phylogenetic, multi-variate, ancestry, and core collection analyses were performed. Farmed cacao germplasm had moderate gene diversity (He = 0.320 ± 0.005) from generally unique trees, but cocoa growing regions were genetically similar. Synonymous matching (16.3%) showed that some clonal material was supplied to farmers. Cacao trees were mainly mixed from Amelonado, Criollo, Iquitos, Contamana, and Marañon ancestries, with predominantly Amelonado-Criollo hybrids. Criollo ancestry, linked to fine or flavour cocoa, was found at more than 30% in 28 unique trees. Forty-five trees, containing the SNP diversity of cacao in Dominica, are recommended as a core germplasm collection. This study identifies promising trees for improving cocoa quality; provides genetic evidence that community, regional, or country-wide pooling would not compromise the exclusive fine or flavour cocoa industry; and discusses other implications towards improving the Dominican cocoa industry.
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Affiliation(s)
- David Gopaulchan
- Cocoa Research Centre, Sir Frank Stockdale Bldg., The University of the West Indies, St. Augustine, 330912, Trinidad, Trinidad and Tobago
| | - Lambert A Motilal
- Cocoa Research Centre, Sir Frank Stockdale Bldg., The University of the West Indies, St. Augustine, 330912, Trinidad, Trinidad and Tobago
| | - Rena K Kalloo
- Cocoa Research Centre, Sir Frank Stockdale Bldg., The University of the West Indies, St. Augustine, 330912, Trinidad, Trinidad and Tobago
| | - Amrita Mahabir
- Cocoa Research Centre, Sir Frank Stockdale Bldg., The University of the West Indies, St. Augustine, 330912, Trinidad, Trinidad and Tobago
| | - Marissa Moses
- Cocoa Research Centre, Sir Frank Stockdale Bldg., The University of the West Indies, St. Augustine, 330912, Trinidad, Trinidad and Tobago
| | - Franklyn Joseph
- The Ministry of Agriculture, Land and Fisheries, the Government of the Commonwealth of Dominica
| | - Pathmanathan Umaharan
- Cocoa Research Centre, Sir Frank Stockdale Bldg., The University of the West Indies, St. Augustine, 330912, Trinidad, Trinidad and Tobago
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Rodriguez-Medina C, Arana AC, Sounigo O, Argout X, Alvarado GA, Yockteng R. Cacao breeding in Colombia, past, present and future. BREEDING SCIENCE 2019; 69:373-382. [PMID: 31598069 PMCID: PMC6776146 DOI: 10.1270/jsbbs.19011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/24/2019] [Indexed: 06/02/2023]
Abstract
Cacao (Theobroma cacao L.) is considered a key crop in Colombian social programs aiming at alleviating rural poverty, promoting peace in post-conflict regions and, replacing crops used for illicit purposes. Colombia is thought to be part of the center of origin of cacao; several germplasm collecting expeditions have been implemented, dating back to the 1940s. Despite that history, the first breeding program based on creating, selecting, and releasing full-sib progenies made extensive use of accessions introduced from other countries as parents. A new breeding strategy was adopted in the 1990s, based on mass selection of promising trees (high-yield and disease-resistant) in farmers' fields, resulting in the selection of clones released to farmers as planting material. In 2012, a new strategy, Recurrent Selection, was adopted by the Colombian Corporation for Agricultural Research, Agrosavia, based on the development of improved populations and allowing the selection of clones at the end of each cycle of recombination. The use of molecular markers is being integrated into this program in order to assist breeders in selecting material. This review provides details about the history and perspectives of the cacao breeding program in Colombia.
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Affiliation(s)
- Caren Rodriguez-Medina
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia; Centro de Investigación Palmira;
Diagonal a la intersección de la carrera 36 con calle 23; Palmira, Valle del Cauca,
Colombia
| | - Alvaro Caicedo Arana
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia; Centro de Investigación Palmira;
Diagonal a la intersección de la carrera 36 con calle 23; Palmira, Valle del Cauca,
Colombia
| | - Olivier Sounigo
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia; Centro de Investigación Palmira;
Diagonal a la intersección de la carrera 36 con calle 23; Palmira, Valle del Cauca,
Colombia
- CIRAD, UPR Bioagresseurs;
Palmira, Valle del Cauca,
Colombia
| | - Xavier Argout
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia; Centro de Investigación Palmira;
Diagonal a la intersección de la carrera 36 con calle 23; Palmira, Valle del Cauca,
Colombia
- CIRAD, UMR AGAP;
Palmira, Valle del Cauca,
Colombia
- Univ. Montpellier, CIRAD, INRA;
Montpellier SupAgro; Montpellier,
France
| | - Gabriel Alvarado Alvarado
- Corporación Universitaria Santa Rosa de Cabal (UNISARC);
Km 4 vía Santa Rosa de Cabal; Risaralda,
Colombia
| | - Roxana Yockteng
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia; Centro de Investigación Tibaitatá;
Km 14 vía a Mosquera; Cundinamarca,
Colombia
- Biodiversité-UMR-CNRS 7205; National Museum of Natural History;
Paris,
France
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Gopaulchan D, Motilal LA, Bekele FL, Clause S, Ariko JO, Ejang HP, Umaharan P. Morphological and genetic diversity of cacao ( Theobroma cacao L.) in Uganda. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:361-375. [PMID: 30956420 PMCID: PMC6419697 DOI: 10.1007/s12298-018-0632-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
Cocoa is among the top foreign exchange earners in Uganda's agriculture sector and has benefitted the livelihood of farmers involved in production. Although cacao cultivation was adopted in the early 1900s, little is known about the on-farm diversity of the crop. A total of 125 cacao landraces were surveyed from eight districts in the Central and Western Regions to evaluate the morphological and genetic diversity of cacao in Uganda. Passport data included site, tree, fruit and seed information. Trees were genotyped using 96 single nucleotide polymorphism markers on a Fluidigm platform. Low heterozygosity was detected in the germplasm in both the Central [observed heterozygosity (H o ) = 0.295, expected heterozygosity (H e) = 0.334] and Western Regions (H o = 0.317, H e = 0.322). Genetic variation in both regions was generally comparable but the regions could be differentiated from each other. Inbreeding was noted in the Central Region while a greater sharing of genetic material was observed in the Western Region. The morphological and genetic data indicated that the Ugandan collection was an interspersed group with low to moderate variation with some separation of the Central from Western regions. Ancestry analysis indicated that the majority of the accessions were hybrids of Marañon lineage but also had Amelonado and Iquitos genetic backgrounds. These findings are consistent with the history of the movement of cacao into Uganda. A core collection of 18 individuals to represent the genetic diversity as well as 12 additional trees with possible advantageous traits is proposed.
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Affiliation(s)
- David Gopaulchan
- Cocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, 330912 Republic of Trinidad and Tobago
| | - Lambert A. Motilal
- Cocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, 330912 Republic of Trinidad and Tobago
| | - Frances L. Bekele
- Cocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, 330912 Republic of Trinidad and Tobago
| | - Séverine Clause
- Sunshine Agro Products Ltd, 24, Avenue de la Toison d’Or, 1050 Brussels, Belgium
| | - James O. Ariko
- Sunshine Agro Products Ltd, 24, Avenue de la Toison d’Or, 1050 Brussels, Belgium
| | - Harriet P. Ejang
- Sunshine Agro Products Ltd, 24, Avenue de la Toison d’Or, 1050 Brussels, Belgium
| | - Pathmanathan Umaharan
- Cocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, 330912 Republic of Trinidad and Tobago
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Cornejo OE, Yee MC, Dominguez V, Andrews M, Sockell A, Strandberg E, Livingstone D, Stack C, Romero A, Umaharan P, Royaert S, Tawari NR, Ng P, Gutierrez O, Phillips W, Mockaitis K, Bustamante CD, Motamayor JC. Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into its domestication process. Commun Biol 2018; 1:167. [PMID: 30345393 PMCID: PMC6191438 DOI: 10.1038/s42003-018-0168-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 09/14/2018] [Indexed: 01/24/2023] Open
Abstract
Domestication has had a strong impact on the development of modern societies. We sequenced 200 genomes of the chocolate plant Theobroma cacao L. to show for the first time to our knowledge that a single population, the Criollo population, underwent strong domestication ~3600 years ago (95% CI: 2481-13,806 years ago). We also show that during the process of domestication, there was strong selection for genes involved in the metabolism of the colored protectants anthocyanins and the stimulant theobromine, as well as disease resistance genes. Our analyses show that domesticated populations of T. cacao (Criollo) maintain a higher proportion of high-frequency deleterious mutations. We also show for the first time the negative consequences of the increased accumulation of deleterious mutations during domestication on the fitness of individuals (significant reduction in kilograms of beans per hectare per year as Criollo ancestry increases, as estimated from a GLM, P = 0.000425).
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Affiliation(s)
- Omar E Cornejo
- School of Biological Sciences, Washington State University, PO Box 644236, Heald Hall 429B, Pullman, Washington, 99164, USA
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, CA, 94305, USA
| | - Muh-Ching Yee
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, CA, 94305, USA
- Stanford Functional Genomics Facility, Stanford, CA, 94305, USA
| | - Victor Dominguez
- Department of Biology, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA
| | - Mary Andrews
- Department of Biology, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA
| | - Alexandra Sockell
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, CA, 94305, USA
| | - Erika Strandberg
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, CA, 94305, USA
- Biomedical Informatics Training Program, 1265 Welch Road, MSOB, X-215, MC 5479, Stanford, CA, 94305-5479, USA
| | - Donald Livingstone
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
| | - Conrad Stack
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Alberto Romero
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Pathmanathan Umaharan
- Cocoa Research Centre, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Stefan Royaert
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Nilesh R Tawari
- Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Pauline Ng
- Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Osman Gutierrez
- SHRS, USDS-ARS, 13601 Old Cutler Road, Miami, FL, 33158, USA
| | - Wilbert Phillips
- Programa de Mejoramiento de Cacao, CATIE, 7170, Turrialba, Costa Rica
| | - Keithanne Mockaitis
- Department of Biology, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA
- Pervasive Technology Institute, Indiana University, 2709 E. 10th St., Bloomington, IN, 47408, USA
| | - Carlos D Bustamante
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, CA, 94305, USA
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Cocoa bean (Theobroma cacao L.) phenolic extracts as PTP1B inhibitors, hepatic HepG2 and pancreatic β-TC3 cell cytoprotective agents and their influence on oxidative stress in rats. Food Res Int 2016. [DOI: 10.1016/j.foodres.2016.01.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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13
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Aseptic artificial fermentation of cocoa beans can be fashioned to replicate the peptide profile of commercial cocoa bean fermentations. Food Res Int 2016; 89:764-772. [DOI: 10.1016/j.foodres.2016.10.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/10/2016] [Accepted: 10/10/2016] [Indexed: 11/24/2022]
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Oracz J, Zyzelewicz D, Nebesny E. The content of polyphenolic compounds in cocoa beans (Theobroma cacao L.), depending on variety, growing region, and processing operations: a review. Crit Rev Food Sci Nutr 2016; 55:1176-92. [PMID: 24915346 DOI: 10.1080/10408398.2012.686934] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Polyphenols form the largest group of compounds among natural antioxidants, which largely affect the overall antioxidant and anti-free radical activity of cocoa beans. The qualitative and quantitative composition of individual fractions of polyphenolic compounds, even within one species, is very diverse and depends on many factors, mainly on the area of cocoa trees cultivation, bean maturity, climatic conditions during growth, and the harvest season and storage time after harvest. Thermal processing of cocoa beans and cocoa derivative products at relatively high temperatures may in addition to favorable physicochemical, microbiological, and organoleptic changes result in a decrease of polyphenols concentration. Technological processing of cocoa beans negatively affects the content of polyphenolic compounds.
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Affiliation(s)
- Joanna Oracz
- a Faculty of Biotechnology and Food Sciences , Lodz University of Technology , Lodz , Poland
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Badrie N, Bekele F, Sikora E, Sikora M. Cocoa agronomy, quality, nutritional, and health aspects. Crit Rev Food Sci Nutr 2016; 55:620-59. [PMID: 24915358 DOI: 10.1080/10408398.2012.669428] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The history of cocoa and chocolate including the birth and the expansion of the chocolate industry was described. Recent developments in the industry and cocoa economy were briefly depicted. An overview of the classification of cacao as well as studies on phenotypic and genetic diversity was presented. Cocoa agronomic practices including traditional and modern propagation techniques were reviewed. Nutrition-related health benefits derived from cocoa consumption were listed and widely reviewed. The specific action of cocoa antioxidants was compared to those of teas and wines. Effects of adding milk to chocolate and chocolate drinks versus bioavailability of cocoa polyphenols were discussed. Finally, flavor, sensory, microbiological, and toxicological aspects of cocoa consumption were presented.
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Affiliation(s)
- Neela Badrie
- a Faculty of Food and Agriculture, Department of Food Production , The University of the West Indies , St. Augustine , Republic of Trinidad and Tobago
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Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil. PLoS One 2015; 10:e0145276. [PMID: 26675449 PMCID: PMC4682715 DOI: 10.1371/journal.pone.0145276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 12/02/2015] [Indexed: 11/19/2022] Open
Abstract
Bahia is the most important cacao-producing state in Brazil, which is currently the sixth-largest country worldwide to produce cacao seeds. In the eighteenth century, the Comum, Pará and Maranhão varieties of cacao were introduced into southern Bahia, and their descendants, which are called ‘Bahian cacao’ or local Bahian varieties, have been cultivated for over 200 years. Comum plants have been used to start plantations in African countries and extended as far as countries in South Asia and Oceania. In Brazil, two sets of clones selected from Bahian varieties and their mutants, the Agronomic Institute of East (SIAL) and Bahian Cacao Institute (SIC) series, represent the diversity of Bahian cacao in germplasm banks. Because the genetic diversity of Bahian varieties, which is essential for breeding programs, remains unknown, the objective of this work was to assess the genetic structure and diversity of local Bahian varieties collected from farms and germplasm banks. To this end, 30 simple sequence repeat (SSR) markers were used to genotype 279 cacao plants from germplasm and local farms. The results facilitated the identification of 219 cacao plants of Bahian origin, and 51 of these were SIAL or SIC clones. Bahian cacao showed low genetic diversity. It could be verified that SIC and SIAL clones do not represent the true diversity of Bahian cacao, with the greatest amount of diversity found in cacao trees on the farms. Thus, a core collection to aid in prioritizing the plants to be sampled for Bahian cacao diversity is suggested. These results provide information that can be used to conserve Bahian cacao plants and applied in breeding programs to obtain more productive Bahian cacao with superior quality and tolerance to major diseases in tropical cacao plantations worldwide.
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Albertini B, Schoubben A, Guarnaccia D, Pinelli F, Della Vecchia M, Ricci M, Di Renzo GC, Blasi P. Effect of fermentation and drying on cocoa polyphenols. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:9948-9953. [PMID: 26086521 DOI: 10.1021/acs.jafc.5b01062] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Cocoa seed polyphenols have demonstrated interesting beneficial effects in humans. Most polyphenols contained in fresh seeds are chemically modified during fermentation, drying, and cocoa powder or chocolate production. The improvement of these procedures to obtain a high-polyphenol-content cocoa is highly desirable. To this aim, a field investigation on the effect of fermentation and natural drying on fine flavor National cocoa (cacao Nacional) was performed. Cocoa seeds were fermented for 6 days and, every day, samples were sun-dried and analyzed for polyphenol content and antioxidant power. During the first 2 days of fermentation, Folin-Ciocalteu and FRAP tests evidenced a significant reduction of polyphenol content and antioxidant capacity, respectively. Changes during the following days of fermentation were less significant. Epicatechin, the most studied member of the catechin family, followed a similar pathway of degradation. Data confirmed the high impact of fermentation and drying on cocoa seed polyphenols. Fermentation and drying are, on the one hand, necessary to obtain cocoa flavor and palatability but, on the other hand, are responsible for greatly compromising polyphenol content. To obtain high-polyphenol-content cocoa, the existing fermentation, drying, and manufacturing protocols should be scientifically reviewed to understand and modify the critical steps.
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Affiliation(s)
- Barbara Albertini
- Department of Pharmaceutical Sciences, University of Perugia , 06123 Perugia, Italy
| | - Aurélie Schoubben
- Department of Pharmaceutical Sciences, University of Perugia , 06123 Perugia, Italy
| | - Davide Guarnaccia
- Laerbium Pharma S.r.l., Via Togliatti n. 73/A, 06073 Corciano, Perugia, Italy
| | - Filippo Pinelli
- European Network "The chocolate way", Via XX Settembre 43, 06124 Perugia, Italy
| | - Mirco Della Vecchia
- Accademia Maestri Cioccolatieri Italiani, Via Sass Muss 6, 32037 Sospirolo, Belluno, Italy
| | - Maurizio Ricci
- Department of Pharmaceutical Sciences, University of Perugia , 06123 Perugia, Italy
| | - Gian Carlo Di Renzo
- Department of Surgical and Biomedical Sciences, S. M. della Misericordia Hospital , S. Andrea delle Fratte, 06156 Perugia, Italy
| | - Paolo Blasi
- School of Pharmacy, University of Camerino , Via Sant'Agostino 1, 62032 Camerino, Italy
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Livingstone D, Royaert S, Stack C, Mockaitis K, May G, Farmer A, Saski C, Schnell R, Kuhn D, Motamayor JC. Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao. DNA Res 2015; 22:279-91. [PMID: 26070980 PMCID: PMC4535616 DOI: 10.1093/dnares/dsv009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 05/01/2015] [Indexed: 11/13/2022] Open
Abstract
Theobroma cacao, the key ingredient in chocolate production, is one of the world's most important tree fruit crops, with ∼4,000,000 metric tons produced across 50 countries. To move towards gene discovery and marker-assisted breeding in cacao, a single-nucleotide polymorphism (SNP) identification project was undertaken using RNAseq data from 16 diverse cacao cultivars. RNA sequences were aligned to the assembled transcriptome of the cultivar Matina 1-6, and 330,000 SNPs within coding regions were identified. From these SNPs, a subset of 6,000 high-quality SNPs were selected for inclusion on an Illumina Infinium SNP array: the Cacao6kSNP array. Using Cacao6KSNP array data from over 1,000 cacao samples, we demonstrate that our custom array produces a saturated genetic map and can be used to distinguish among even closely related genotypes. Our study enhances and expands the genetic resources available to the cacao research community, and provides the genome-scale set of tools that are critical for advancing breeding with molecular markers in an agricultural species with high genetic diversity.
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Affiliation(s)
| | | | | | | | - Greg May
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Christopher Saski
- Clemson University Genomics and Computational Biology Laboratory, Institute for Translational Genomics, Clemson, SC 29634, USA
| | | | - David Kuhn
- United States Department of Agriculture-Agriculture Research Service, Subtropical, Horticulture Research Station, Miami, FL 33158, USA
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Herrmann L, Haase I, Blauhut M, Barz N, Fischer M. DNA-based differentiation of the Ecuadorian cocoa types CCN-51 and Arriba based on sequence differences in the chloroplast genome. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:12118-12127. [PMID: 25404556 DOI: 10.1021/jf504258w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Two cocoa types, Arriba and CCN-51, are being cultivated in Ecuador. With regard to the unique aroma, Arriba is considered a fine cocoa type, while CCN-51 is a bulk cocoa because of its weaker aroma. Because it is being assumed that Arriba is mixed with CCN-51, there is an interest in the analytical differentiation of the two types. Two methods to identify CCN-51 adulterations in Arriba cocoa were developed on the basis of differences in the chloroplast DNA. On the one hand, a different repeat of the sequence TAAAG in the inverted repeat region results in a different length of amplicons for the two cocoa types, which can be detected by agarose gel electrophoresis, capillary gel electrophoresis, and denaturing high-performance liquid chromatography. On the other hand, single nucleotide polymorphisms (SNPs) between the CCN-51 and Arriba sequences represent restriction sites, which can be used for restriction fragment length polymorphism analysis. A semi-quantitative analysis based on these SNPs is feasible. A method for an exact quantitation based on these results is not realizable. These sequence variations were confirmed for a comprehensive cultivar collection of Arriba and CCN-51, for both bean and leaf samples.
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Affiliation(s)
- Luise Herrmann
- Hamburg School of Food Science, Institut für Lebensmittelchemie, Universität Hamburg , Grindelallee 117, 20146 Hamburg, Germany
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Chumacero de Schawe C, Durka W, Tscharntke T, Hensen I, Kessler M. Gene flow and genetic diversity in cultivated and wild cacao (Theobroma cacao) in Bolivia. AMERICAN JOURNAL OF BOTANY 2013; 100:2271-2279. [PMID: 24158148 DOI: 10.3732/ajb.1300025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY The role of pollen flow within and between cultivated and wild tropical crop species is little known. To study the pollen flow of cacao, we estimated the degree of self-pollination and pollen dispersal distances as well as gene flow between wild and cultivated cacao (Theobroma cacao L.). METHODS We studied pollen flow and genetic diversity of cultivated and wild cacao populations by genotyping 143 wild and 86 cultivated mature plants and 374 seedlings raised from 19 wild and 25 cultivated trees at nine microsatellite loci. KEY RESULTS A principal component analysis distinguished wild and cultivated cacao trees, supporting the notion that Bolivia harbors truly wild cacao populations. Cultivated cacao had a higher level of genetic diversity than wild cacao, presumably reflecting the varied origin of cultivated plants. Both cacao types had high outcrossing rates, but the paternity analysis revealed 7-14% self-pollination in wild and cultivated cacao. Despite the tiny size of the pollinators, pollen was transported distances up to 3 km; wild cacao showed longer distances (mean = 922 m) than cultivated cacao (826 m). Our data revealed that 16-20% of pollination events occurred between cultivated and wild populations. CONCLUSIONS We found evidence of self-pollination in both wild and cultivated cacao. Pollination distances are larger than those typically reported in tropical understory tree species. The relatively high pollen exchange from cultivated to wild cacao compromises genetic identity of wild populations, calling for the protection of extensive natural forest tracts to protect wild cacao in Bolivia.
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21
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Sveinsson S, Gill N, Kane NC, Cronk Q. Transposon fingerprinting using low coverage whole genome shotgun sequencing in cacao (Theobroma cacao L.) and related species. BMC Genomics 2013; 14:502. [PMID: 23883295 PMCID: PMC3726317 DOI: 10.1186/1471-2164-14-502] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 07/19/2013] [Indexed: 01/24/2023] Open
Abstract
Background Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characterizing crop germplasm. However, their repetitive nature makes them challenging to study using conventional methods of molecular biology. Next generation sequencing and new computational tools have greatly facilitated the investigation of TE variation within species and among closely related species. Results (i) We generated low-coverage Illumina whole genome shotgun sequencing reads for multiple individuals of cacao (Theobroma cacao) and related species. These reads were analysed using both an alignment/mapping approach and a de novo (graph based clustering) approach. (ii) A standard set of ultra-conserved orthologous sequences (UCOS) standardized TE data between samples and provided phylogenetic information on the relatedness of samples. (iii) The mapping approach proved highly effective within the reference species but underestimated TE abundance in interspecific comparisons relative to the de novo methods. (iv) Individual T. cacao accessions have unique patterns of TE abundance indicating that the TE composition of the genome is evolving actively within this species. (v) LTR/Gypsy elements are the most abundant, comprising c.10% of the genome. (vi) Within T. cacao the retroelement families show an order of magnitude greater sequence variability than the DNA transposon families. (vii) Theobroma grandiflorum has a similar TE composition to T. cacao, but the related genus Herrania is rather different, with LTRs making up a lower proportion of the genome, perhaps because of a massive presence (c. 20%) of distinctive low complexity satellite-like repeats in this genome. Conclusions (i) Short read alignment/mapping to reference TE contigs provides a simple and effective method of investigating intraspecific differences in TE composition. It is not appropriate for comparing repetitive elements across the species boundaries, for which de novo methods are more appropriate. (ii) Individual T. cacao accessions have unique spectra of TE composition indicating active evolution of TE abundance within this species. TE patterns could potentially be used as a “fingerprint” to identify and characterize cacao accessions.
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Affiliation(s)
- Saemundur Sveinsson
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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22
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Motamayor JC, Mockaitis K, Schmutz J, Haiminen N, III DL, Cornejo O, Findley SD, Zheng P, Utro F, Royaert S, Saski C, Jenkins J, Podicheti R, Zhao M, Scheffler BE, Stack JC, Feltus FA, Mustiga GM, Amores F, Phillips W, Marelli JP, May GD, Shapiro H, Ma J, Bustamante CD, Schnell RJ, Main D, Gilbert D, Parida L, Kuhn DN. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol 2013; 14:r53. [PMID: 23731509 PMCID: PMC4053823 DOI: 10.1186/gb-2013-14-6-r53] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 04/09/2013] [Accepted: 06/03/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders. RESULTS We describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina 1-6. The genome of the Matina 1-6 cultivar is 445 Mbp, which is significantly larger than a sequenced Criollo cultivar, and more typical of other cultivars. The chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 Mbp, with a contig N50 of 84.4 kbp, a scaffold N50 of 34.4 Mbp, and an evidence-based gene set of 29,408 loci. Version 1.1 has 10x the scaffold N50 and 4x the contig N50 as Criollo, and includes 111 Mb more anchored sequence. The version 1.1 assembly has 4.4% gap sequence, while Criollo has 10.9%. Through a combination of haplotype, association mapping and gene expression analyses, we leverage this robust reference genome to identify a promising candidate gene responsible for pod color variation. We demonstrate that green/red pod color in cacao is likely regulated by the R2R3 MYB transcription factor TcMYB113, homologs of which determine pigmentation in Rosaceae, Solanaceae, and Brassicaceae. One SNP within the target site for a highly conserved trans-acting siRNA in dicots, found within TcMYB113, seems to affect transcript levels of this gene and therefore pod color variation. CONCLUSIONS We report a high-quality sequence and annotation of Theobroma cacao L. and demonstrate its utility in identifying candidate genes regulating traits.
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Affiliation(s)
| | - Keithanne Mockaitis
- Department of Biology, and Center for Genomics and Bioinformatics, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA
| | - Jeremy Schmutz
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, AL, 35806, USA
| | - Niina Haiminen
- IBM T J Watson Research, Yorktown Heights, NY, 10598, USA
| | - Donald Livingstone III
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
| | - Omar Cornejo
- Department of Genetics, Stanford University, 300 Pasteur Dr, Stanford, CA, 94305, USA
| | - Seth D Findley
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Ping Zheng
- Department of Horticulture, Washington State University, Johnson Hall, Pullman, WA, 99164, USA
| | - Filippo Utro
- IBM T J Watson Research, Yorktown Heights, NY, 10598, USA
| | - Stefan Royaert
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
| | - Christopher Saski
- Clemson University Genomics Institute, 105 Collings Street, Clemson, SC, 29634, USA
| | - Jerry Jenkins
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, AL, 35806, USA
| | - Ram Podicheti
- Center for Genomics and Bioinformatics and School of Informatics and Computing, Indiana University, 919 E 10th St, Bloomington, IN, 47408, USA
| | - Meixia Zhao
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Brian E Scheffler
- United States Department of Agriculture-Agriculture Research Service, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - Joseph C Stack
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Frank A Feltus
- Clemson University Genomics Institute, 105 Collings Street, Clemson, SC, 29634, USA
| | | | - Freddy Amores
- Estación Experimental Tropical Pichilingue, Instituto Nacional Autónomo de Investigaciones Agropecuarias (INIAP), Código Postal 24, Km 5 vía Quevedo - El Empalme, Quevedo, Ecuador
| | - Wilbert Phillips
- Programa de Mejoramiento de Cacao, CATIE 7170, Turrialba, Costa Rica
| | | | - Gregory D May
- National Center for Genome Resources, 2935 Rodeo Park Drive E, Santa Fe, NM, 87505, USA
| | - Howard Shapiro
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University, 300 Pasteur Dr, Stanford, CA, 94305, USA
| | - Raymond J Schnell
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Johnson Hall, Pullman, WA, 99164, USA
| | - Don Gilbert
- Department of Biology, and Center for Genomics and Bioinformatics, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA
| | - Laxmi Parida
- IBM T J Watson Research, Yorktown Heights, NY, 10598, USA
| | - David N Kuhn
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
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Saltini R, Akkerman R, Frosch S. Optimizing chocolate production through traceability: A review of the influence of farming practices on cocoa bean quality. Food Control 2013. [DOI: 10.1016/j.foodcont.2012.05.054] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Miller AJ, Gross BL. From forest to field: perennial fruit crop domestication. AMERICAN JOURNAL OF BOTANY 2011; 98:1389-414. [PMID: 21865506 DOI: 10.3732/ajb.1000522] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
PREMISE OF THE STUDY Archaeological and genetic analyses of seed-propagated annual crops have greatly advanced our understanding of plant domestication and evolution. Comparatively little is known about perennial plant domestication, a relevant topic for understanding how genes and genomes evolve in long-lived species, and how perennials respond to selection pressures operating on a relatively short time scale. Here, we focus on long-lived perennial crops (mainly trees and other woody plants) grown for their fruits. KEY RESULTS We reviewed (1) the basic biology of long-lived perennials, setting the stage for perennial domestication by considering how these species evolve in nature; (2) the suite of morphological features associated with perennial fruit crops undergoing domestication; (3) the origins and evolution of domesticated perennials grown for their fruits; and (4) the genetic basis of domestication in perennial fruit crops. CONCLUSIONS Long-lived perennials have lengthy juvenile phases, extensive outcrossing, widespread hybridization, and limited population structure. Under domestication, these features, combined with clonal propagation, multiple origins, and ongoing crop-wild gene flow, contribute to mild domestication bottlenecks in perennial fruit crops. Morphological changes under domestication have many parallels to annual crops, but with key differences for mating system evolution and mode of reproduction. Quantitative trait loci associated with domestication traits in perennials are mainly of minor effect and may not be stable across years. Future studies that take advantage of genomic approaches and consider demographic history will elucidate the genetics of agriculturally and ecologically important traits in perennial fruit crops and their wild relatives.
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Affiliation(s)
- Allison J Miller
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, Saint Louis, Missouri 63103 USA.
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Trognitz B, Scheldeman X, Hansel-Hohl K, Kuant A, Grebe H, Hermann M. Genetic population structure of cacao plantings within a young production area in Nicaragua. PLoS One 2011; 6:e16056. [PMID: 21264251 PMCID: PMC3021531 DOI: 10.1371/journal.pone.0016056] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 12/06/2010] [Indexed: 11/29/2022] Open
Abstract
Significant cocoa production in the municipality of Waslala, Nicaragua, began in 1961. Since the 1980s, its economic importance to rural smallholders increased, and the region now contributes more than 50% of national cocoa bean production. This research aimed to assist local farmers to develop production of high-value cocoa based on optimal use of cacao biodiversity. Using microsatellite markers, the allelic composition and genetic structure of cacao was assessed from 44 representative plantings and two unmanaged trees. The population at Waslala consists of only three putative founder genotype spectra (lineages). Two (B and R) were introduced during the past 50 years and occur in >95% of all trees sampled, indicating high rates of outcrossing. Based on intermediate allelic diversity, there was large farm-to-farm multilocus genotypic variation. GIS analysis revealed unequal distribution of the genotype spectra, with R being frequent within a 2 km corridor along roads, and B at more remote sites with lower precipitation. The third lineage, Y, was detected in the two forest trees. For explaining the spatial stratification of the genotype spectra, both human intervention and a combination of management and selection driven by environmental conditions, appear responsible. Genotypes of individual trees were highly diverse across plantings, thus enabling selection for farm-specific qualities. On-farm populations can currently be most clearly recognized by the degree of the contribution of the three genotype spectra. Of two possible strategies for future development of cacao in Waslala, i.e. introducing more unrelated germplasm, or working with existing on-site diversity, the latter seems most appropriate. Superior genotypes could be selected by their specific composite genotype spectra as soon as associations with desired quality traits are established, and clonally multiplied. The two Y trees from the forest share a single multilocus genotype, possibly representing the Mayan, 'ancient Criollo' cacao.
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Affiliation(s)
- Bodo Trognitz
- Austrian Institute of Technology, Seibersdorf, Austria.
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Abstract
We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.
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Motamayor JC, Lachenaud P, da Silva E Mota JW, Loor R, Kuhn DN, Brown JS, Schnell RJ. Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L). PLoS One 2008; 3:e3311. [PMID: 18827930 PMCID: PMC2551746 DOI: 10.1371/journal.pone.0003311] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 08/29/2008] [Indexed: 11/19/2022] Open
Abstract
Numerous collecting expeditions of Theobroma cacao L. germplasm have been undertaken in Latin-America. However, most of this germplasm has not contributed to cacao improvement because its relationship to cultivated selections was poorly understood. Germplasm labeling errors have impeded breeding and confounded the interpretation of diversity analyses. To improve the understanding of the origin, classification, and population differentiation within the species, 1241 accessions covering a large geographic sampling were genotyped with 106 microsatellite markers. After discarding mislabeled samples, 10 genetic clusters, as opposed to the two genetic groups traditionally recognized within T. cacao, were found by applying Bayesian statistics. This leads us to propose a new classification of the cacao germplasm that will enhance its management. The results also provide new insights into the diversification of Amazon species in general, with the pattern of differentiation of the populations studied supporting the palaeoarches hypothesis of species diversification. The origin of the traditional cacao cultivars is also enlightened in this study.
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Affiliation(s)
- Juan C Motamayor
- National Germplasm Repository, US Department of Agriculture, Agricultural Research Service, Subtropical Horticulture Research Station, Miami, Florida, USA.
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Schnell RJ, Kuhn DN, Brown JS, Olano CT, Phillips-Mora W, Amores FM, Motamayor JC. Development of a marker assisted selection program for cacao. PHYTOPATHOLOGY 2007; 97:1664-9. [PMID: 18943731 DOI: 10.1094/phyto-97-12-1664] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
ABSTRACT Production of cacao in tropical America has been severely affected by fungal pathogens causing diseases known as witches' broom (WB, caused by Moniliophthora perniciosa), frosty pod (FP, caused by M. roreri) and black pod (BP, caused by Phytophthora spp.). BP is pan-tropical and causes losses in all producing areas. WB is found in South America and parts of the Caribbean, while FP is found in Central America and parts of South America. Together, these diseases were responsible for over 700 million US dollars in losses in 2001 (4). Commercial cacao production in West Africa and South Asia are not yet affected by WB and FP, but cacao grown in these regions is susceptible to both. With the goal of providing new disease resistant cultivars the USDA-ARS and Mars, Inc. have developed a marker assisted selection (MAS) program. Quantitative trait loci have been identified for resistance to WB, FP, and BP. The potential usefulness of these markers in identifying resistant individuals has been confirmed in an experimental F(1) family in Ecuador.
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Zhang D, Boccara M, Motilal L, Butler DR, Umaharan P, Mischke S, Meinhardt L. Microsatellite variation and population structure in the “Refractario” cacao of Ecuador. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9345-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Marcano M, Pugh T, Cros E, Morales S, Portillo Páez EA, Courtois B, Glaszmann JC, Engels JMM, Phillips W, Astorga C, Risterucci AM, Fouet O, González V, Rosenberg K, Vallat I, Dagert M, Lanaud C. Adding value to cocoa (Theobroma cacao L.) germplasm information with domestication history and admixture mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:877-84. [PMID: 17252253 DOI: 10.1007/s00122-006-0486-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Accepted: 12/16/2006] [Indexed: 05/13/2023]
Abstract
A sound understanding of crop history can provide the basis for deriving novel genetic information through admixture mapping. We confirmed this, by using characterization data from an international collection of cocoa, collected 25 years ago, and from a contemporary plantation. We focus on the trees derived from three centuries of admixture between Meso-American Criollo and South American Forastero genomes. In both cacao sets of individuals, linkage disequilibrium extended over long genetic distances along chromosome regions, as expected in populations derived from recent admixture. Based on loose genome scans, genomic regions involved in useful traits were identified. Fifteen genomic regions involved in seed and fruit weight variation were highlighted. They correspond to ten previously identified QTLs and five novel ones. Admixture mapping can help to add value to genetic resources and thus, help to encourage investment in their conservation.
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Affiliation(s)
- Maria Marcano
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, (CIRAD) TA 40/03, 34398, Montpellier Cedex 5, France.
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BORRONE JAMESW, BROWN JSTEVEN, KUHN DAVIDN, MOTAMAYOR JUANC, SCHNELL RAYMONDJ. Microsatellite markers developed fromTheobroma cacaoL. expressed sequence tags. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2006.01561.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Zhang D, Arevalo-Gardini E, Mischke S, Zúñiga-Cernades L, Barreto-Chavez A, Del Aguila JA. Genetic diversity and structure of managed and semi-natural populations of cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru. ANNALS OF BOTANY 2006; 98:647-55. [PMID: 16845139 PMCID: PMC3292056 DOI: 10.1093/aob/mcl146] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Cocoa (Theobroma cacao) is indigenous to the Amazon region of South America, and it is well known that the Peruvian Amazon harbours a large number of diverse cocoa populations. A small fraction of the diversity has been collected and maintained as an ex-situ germplasm repository in Peru. However, incorrect labelling of accessions and lack of information on genetic diversity have hindered efficient conservation and use of this germplasm. This study targeted assessment of genetic diversity and population structure in a managed and a semi-natural population. METHODS Using a capillary electrophoresis genotyping system, 105 cocoa accessions collected from the Huallaga and Ucayali valleys of Peru were fingerprinted. Based on 15 loci SSR profiles, genetic identity was examined for each accession and duplicates identified, population structure assessed and genetic diversity analysed in these two populations. KEY RESULTS Ten synonymous mislabelled groups were identified among the 105 accessions. The germplasm group in the Huallaga valley was clearly separated from the group in Ucayali valley by the Bayesian assignment test. The Huallaga group has lower genetic diversity, both in terms of allelic richness and of gene diversity, than the Ucayali group. Analysis of molecular variance suggested genetic substructure in the Ucayali group. Significant spatial correlation between genetic distance and geographical distances was detected in the Ucayali group by Mantel tests. CONCLUSIONS These results substantiate the hypothesis that the Peruvian Amazon hosts a high level of cocoa genetic diversity, and the diversity has a spatial structure. The introduction of exotic seed populations into the Peruvian Amazon is changing the cocoa germplasm spectrum in this region. The spatial structure of cocoa diversity recorded here highlights the need for additional collecting and conservation measures for natural and semi-natural cocoa populations.
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Affiliation(s)
- Dapeng Zhang
- USDA ARS PSI SPCL, 10300 Baltimore Avenue, Bldg 050, Rm 100, BARC-W, Beltsville, MD 20705, USA.
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